EHV-1 TSS dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Normalization: VST
TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.
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The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.
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## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF17 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF30 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 1 ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15: 1 ORF53 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17: 1 ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18: 1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20: 1 ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 23: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 24: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 25: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 2 ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33: 2 ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34: 2 ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36: 2 ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43: 2 ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46: 2 ORF41 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49: 2 ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50: 2 ORF48 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51: 2 ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52: 2 ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53: 2 ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54: 2 ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55: 2 ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 56: 2 ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 57: 2 ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 58: 2 ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 59: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 60: 3 ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61: 3 ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62: 3 ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63: 3 ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64: 3 ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65: 3 ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66: 3 ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67: 3 ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68: 3 ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69: 3 ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 70: 3 ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 71: 3 ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 72: 3 NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 73: 3 ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 74: 4 ORF19 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 75: 4 ORF37 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 76: 4 ORF51 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 77: 4 ORF55 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 78: 4 ORF66_1 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 79: 5 ORF64_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.59026662
## 2: 0.002173813 -2.3786533 0.5530091 0.59026662
## 3: 0.002173813 -2.3786533 0.5530091 0.59026662
## 4: 0.002173813 -2.3786533 0.5530091 0.59026662
## 5: 0.002173813 -2.3786533 0.5530091 0.59026662
## 6: 0.002173813 -2.3786533 0.5530091 0.59026662
## 7: 0.002173813 -2.3786533 0.5530091 0.59026662
## 8: 0.002173813 -2.3786533 0.5530091 0.59026662
## 9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002173813 -2.3786533 0.5530091 0.59026662
## 23: 0.002173813 -2.3786533 0.5530091 0.59026662
## 24: 0.002173813 -2.3786533 0.5530091 0.59026662
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.002630562 -1.9748104 0.3778197 0.20208360
## 56: 0.002630562 -1.9748104 0.3778197 0.20208360
## 57: 0.002630562 -1.9748104 0.3778197 0.20208360
## 58: 0.002630562 -1.9748104 0.3778197 0.20208360
## 59: 0.002630562 -1.9748104 0.3778197 0.20208360
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005127433 -0.5566122 0.2345080 0.82739367
## 70: 0.005127433 -0.5566122 0.2345080 0.82739367
## 71: 0.005127433 -0.5566122 0.2345080 0.82739367
## 72: 0.005127433 -0.5566122 0.2345080 0.82739367
## 73: 0.005127433 -0.5566122 0.2345080 0.82739367
## 74: 0.005224449 -1.2350532 1.5108478 0.06845455
## 75: 0.005224449 -1.2350532 1.5108478 0.06845455
## 76: 0.005224449 -1.2350532 1.5108478 0.06845455
## 77: 0.005224449 -1.2350532 1.5108478 0.06845455
## 78: 0.005224449 -1.2350532 1.5108478 0.06845455
## 79: 0.002585386 -1.9080987 0.3087534 0.43210279
## se.bp v c pchi
## [1] "ORF74" "ORF41"## [1] 2## [1] "ORF7" "ORF24" "ORF27" "ORF28" "ORF32" "ORF35" "ORF44" "ORF45"
## [9] "ORF49" "ORF56" "ORF57" "ORF59" "NOIR_1" "ORF76"## [1] 14Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 1 ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15: 1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17: 1 ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24: 2 ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 2 ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33: 2 ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40: 2 ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43: 2 ORF41 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46: 2 ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47: 2 ORF48 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48: 2 ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49: 2 ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50: 2 ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51: 2 ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52: 2 ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53: 2 ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54: 2 ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55: 2 ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 56: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 57: 3 ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 58: 3 ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 59: 3 ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 60: 3 ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61: 3 ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62: 3 ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63: 3 ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64: 3 ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65: 3 ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66: 3 ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67: 3 ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68: 3 ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69: 3 NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 70: 3 ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 71: 4 ORF17 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 72: 4 ORF30 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 73: 4 ORF53 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 74: 5 ORF19 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 75: 5 ORF37 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 76: 5 ORF51 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 77: 5 ORF55 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 78: 5 ORF66_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 79: 6 ORF64_1 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.59026662
## 2: 0.002173813 -2.3786533 0.5530091 0.59026662
## 3: 0.002173813 -2.3786533 0.5530091 0.59026662
## 4: 0.002173813 -2.3786533 0.5530091 0.59026662
## 5: 0.002173813 -2.3786533 0.5530091 0.59026662
## 6: 0.002173813 -2.3786533 0.5530091 0.59026662
## 7: 0.002173813 -2.3786533 0.5530091 0.59026662
## 8: 0.002173813 -2.3786533 0.5530091 0.59026662
## 9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002630562 -1.9748104 0.3778197 0.20208360
## 23: 0.002630562 -1.9748104 0.3778197 0.20208360
## 24: 0.002630562 -1.9748104 0.3778197 0.20208360
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.002630562 -1.9748104 0.3778197 0.20208360
## 56: 0.002630562 -1.9748104 0.3778197 0.20208360
## 57: 0.005127433 -0.5566122 0.2345080 0.82739367
## 58: 0.005127433 -0.5566122 0.2345080 0.82739367
## 59: 0.005127433 -0.5566122 0.2345080 0.82739367
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005127433 -0.5566122 0.2345080 0.82739367
## 70: 0.005127433 -0.5566122 0.2345080 0.82739367
## 71: 0.005224449 -1.2350532 1.5108478 0.06845455
## 72: 0.005224449 -1.2350532 1.5108478 0.06845455
## 73: 0.005224449 -1.2350532 1.5108478 0.06845455
## 74: 0.002585386 -1.9080987 0.3087534 0.43210279
## 75: 0.002585386 -1.9080987 0.3087534 0.43210279
## 76: 0.002585386 -1.9080987 0.3087534 0.43210279
## 77: 0.002585386 -1.9080987 0.3087534 0.43210279
## 78: 0.002585386 -1.9080987 0.3087534 0.43210279
## 79: 0.004830169 -0.9381876 0.3682901 0.16904056
## se.bp v c pchi
## [1] "ORF63" "ORF74" "CTO" "ORF41"## [1] 4## [1] "ORF7" "ORF24" "ORF27" "ORF28" "ORF32" "ORF35" "ORF44"
## [8] "ORF45" "ORF49" "ORF56" "ORF57" "ORF59" "NOIR_1" "ORF76"
## [15] "ORF64_1"## [1] 15Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 1 ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15: 1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17: 1 ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24: 2 ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 2 ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33: 2 ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40: 2 ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45: 2 ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46: 2 ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47: 2 ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48: 2 ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49: 2 ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50: 2 ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51: 2 ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52: 2 ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53: 2 ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55: 3 ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 56: 3 ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 57: 3 ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 58: 3 ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 59: 3 ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 60: 3 ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61: 3 ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62: 3 ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63: 3 ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64: 3 ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65: 3 ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66: 3 ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67: 3 NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68: 3 ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69: 4 ORF17 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 70: 4 ORF30 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 71: 4 ORF53 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 72: 5 ORF19 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 73: 5 ORF37 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 74: 5 ORF51 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 75: 5 ORF55 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 76: 5 ORF66_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 77: 6 ORF41 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 78: 6 ORF48 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 79: 7 ORF64_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.59026662
## 2: 0.002173813 -2.3786533 0.5530091 0.59026662
## 3: 0.002173813 -2.3786533 0.5530091 0.59026662
## 4: 0.002173813 -2.3786533 0.5530091 0.59026662
## 5: 0.002173813 -2.3786533 0.5530091 0.59026662
## 6: 0.002173813 -2.3786533 0.5530091 0.59026662
## 7: 0.002173813 -2.3786533 0.5530091 0.59026662
## 8: 0.002173813 -2.3786533 0.5530091 0.59026662
## 9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002630562 -1.9748104 0.3778197 0.20208360
## 23: 0.002630562 -1.9748104 0.3778197 0.20208360
## 24: 0.002630562 -1.9748104 0.3778197 0.20208360
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.005127433 -0.5566122 0.2345080 0.82739367
## 56: 0.005127433 -0.5566122 0.2345080 0.82739367
## 57: 0.005127433 -0.5566122 0.2345080 0.82739367
## 58: 0.005127433 -0.5566122 0.2345080 0.82739367
## 59: 0.005127433 -0.5566122 0.2345080 0.82739367
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005224449 -1.2350532 1.5108478 0.06845455
## 70: 0.005224449 -1.2350532 1.5108478 0.06845455
## 71: 0.005224449 -1.2350532 1.5108478 0.06845455
## 72: 0.002585386 -1.9080987 0.3087534 0.43210279
## 73: 0.002585386 -1.9080987 0.3087534 0.43210279
## 74: 0.002585386 -1.9080987 0.3087534 0.43210279
## 75: 0.002585386 -1.9080987 0.3087534 0.43210279
## 76: 0.002585386 -1.9080987 0.3087534 0.43210279
## 77: 0.004830169 -0.9381876 0.3682901 0.16904056
## 78: 0.004830169 -0.9381876 0.3682901 0.16904056
## 79: 0.005278328 -1.0831543 0.8420568 0.12160986
## se.bp v c pchi
## [1] "ORF63" "ORF74"## [1] 2## [1] "ORF7" "ORF24" "ORF27" "ORF28" "ORF32" "ORF35" "ORF44" "ORF45"
## [9] "ORF49" "ORF56" "ORF57" "ORF59" "NOIR_1" "ORF76" "ORF41" "ORF48"## [1] 16Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 3 ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32: 3 ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33: 3 ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34: 3 ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35: 3 ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36: 3 ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37: 3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38: 3 ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39: 4 ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40: 4 ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41: 4 ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42: 4 ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43: 4 ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44: 4 ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45: 4 ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46: 4 ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47: 4 ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48: 4 ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49: 4 ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50: 4 ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51: 4 ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52: 4 ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53: 4 ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54: 4 ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55: 5 ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56: 5 ORF24 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57: 5 ORF27 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58: 5 ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59: 5 ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60: 5 ORF35 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61: 5 ORF44 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62: 5 ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 63: 5 ORF49 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 64: 5 ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 65: 5 ORF57 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 66: 5 ORF59 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 67: 5 NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 68: 5 ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 69: 6 ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 70: 6 ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 71: 6 ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 72: 7 ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 73: 7 ORF37 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 74: 7 ORF51 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 75: 7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 76: 8 ORF41 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 77: 8 ORF48 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 78: 9 ORF55 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 79: 10 ORF64_1 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.590266623
## 2: 0.002173813 -2.3786533 0.5530091 0.590266623
## 3: 0.002173813 -2.3786533 0.5530091 0.590266623
## 4: 0.002173813 -2.3786533 0.5530091 0.590266623
## 5: 0.002173813 -2.3786533 0.5530091 0.590266623
## 6: 0.002173813 -2.3786533 0.5530091 0.590266623
## 7: 0.002173813 -2.3786533 0.5530091 0.590266623
## 8: 0.002173813 -2.3786533 0.5530091 0.590266623
## 9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.002585386 -1.9080987 0.3087534 0.432102790
## 63: 0.002585386 -1.9080987 0.3087534 0.432102790
## 64: 0.002585386 -1.9080987 0.3087534 0.432102790
## 65: 0.002585386 -1.9080987 0.3087534 0.432102790
## 66: 0.002585386 -1.9080987 0.3087534 0.432102790
## 67: 0.002585386 -1.9080987 0.3087534 0.432102790
## 68: 0.002585386 -1.9080987 0.3087534 0.432102790
## 69: 0.004830169 -0.9381876 0.3682901 0.169040559
## 70: 0.004830169 -0.9381876 0.3682901 0.169040559
## 71: 0.004830169 -0.9381876 0.3682901 0.169040559
## 72: 0.005278328 -1.0831543 0.8420568 0.121609856
## 73: 0.005278328 -1.0831543 0.8420568 0.121609856
## 74: 0.005278328 -1.0831543 0.8420568 0.121609856
## 75: 0.005278328 -1.0831543 0.8420568 0.121609856
## 76: 0.005181368 -0.8929713 1.1657673 0.068980610
## 77: 0.005181368 -0.8929713 1.1657673 0.068980610
## 78: 0.005202505 -0.4915675 0.2569468 0.451195188
## 79: 0.005277337 -0.4694357 0.4086000 0.002664175
## se.bp v c pchi
## [1] "ORF61" "ORF74" "ORF46" "ORF62" "ORF37"## [1] 5## [1] "ORF4" "ORF5" "ORF9" "ORF38" "ORF50" "ORF63" "ORF65_1"
## [8] "ORF69" "ORF17" "ORF30" "ORF53" "ORF55" "ORF64_1"## [1] 13Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 3 ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32: 3 ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33: 3 ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34: 3 ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35: 3 ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36: 3 ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37: 3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38: 3 ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39: 4 ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40: 4 ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41: 4 ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42: 4 ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43: 4 ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44: 4 ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45: 4 ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46: 4 ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47: 4 ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48: 4 ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49: 4 ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50: 4 ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51: 4 ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52: 4 ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53: 4 ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54: 4 ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55: 5 ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56: 5 ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57: 5 ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58: 5 ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59: 5 ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60: 5 NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61: 5 ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62: 6 ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 63: 6 ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 64: 6 ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 65: 7 ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 66: 7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 67: 8 ORF24 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 68: 8 ORF27 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 69: 8 ORF35 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 70: 8 ORF44 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 71: 8 ORF49 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 72: 8 ORF57 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 73: 8 ORF59 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 74: 9 ORF37 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 75: 9 ORF51 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 76: 10 ORF41 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 77: 10 ORF48 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 78: 11 ORF55 0.6118917 0.8437067 0.6974597 0.033505179 0.0189981734
## 79: 12 ORF64_1 0.5880849 0.8219482 0.7195606 0.034578844 0.0209653160
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.590266623
## 2: 0.002173813 -2.3786533 0.5530091 0.590266623
## 3: 0.002173813 -2.3786533 0.5530091 0.590266623
## 4: 0.002173813 -2.3786533 0.5530091 0.590266623
## 5: 0.002173813 -2.3786533 0.5530091 0.590266623
## 6: 0.002173813 -2.3786533 0.5530091 0.590266623
## 7: 0.002173813 -2.3786533 0.5530091 0.590266623
## 8: 0.002173813 -2.3786533 0.5530091 0.590266623
## 9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.004830169 -0.9381876 0.3682901 0.169040559
## 63: 0.004830169 -0.9381876 0.3682901 0.169040559
## 64: 0.004830169 -0.9381876 0.3682901 0.169040559
## 65: 0.005278328 -1.0831543 0.8420568 0.121609856
## 66: 0.005278328 -1.0831543 0.8420568 0.121609856
## 67: 0.005181368 -0.8929713 1.1657673 0.068980610
## 68: 0.005181368 -0.8929713 1.1657673 0.068980610
## 69: 0.005181368 -0.8929713 1.1657673 0.068980610
## 70: 0.005181368 -0.8929713 1.1657673 0.068980610
## 71: 0.005181368 -0.8929713 1.1657673 0.068980610
## 72: 0.005181368 -0.8929713 1.1657673 0.068980610
## 73: 0.005181368 -0.8929713 1.1657673 0.068980610
## 74: 0.005202505 -0.4915675 0.2569468 0.451195188
## 75: 0.005202505 -0.4915675 0.2569468 0.451195188
## 76: 0.005277337 -0.4694357 0.4086000 0.002664175
## 77: 0.005277337 -0.4694357 0.4086000 0.002664175
## 78: 0.004895109 -0.7634588 0.2463505 0.018100690
## 79: 0.004790086 -0.7521758 0.1706391 0.701623569
## se.bp v c pchi
## [1] "ORF61" "ORF74" "ORF46" "ORF62"## [1] 4## [1] "ORF4" "ORF5" "ORF9" "ORF38" "ORF50" "ORF63" "ORF65_1"
## [8] "ORF69" "ORF17" "ORF30" "ORF53" "ORF37" "ORF51" "ORF41"
## [15] "ORF48" "ORF55" "ORF64_1"## [1] 17Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 2: 1 ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 3: 1 ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 4: 1 ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 5: 1 ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 6: 1 ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 7: 1 ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 8: 1 ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 9: 1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10: 1 ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11: 1 ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12: 1 ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13: 1 NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14: 2 ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15: 2 ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16: 2 ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17: 2 ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18: 2 ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19: 2 ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20: 2 ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21: 2 ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22: 2 ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23: 2 ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24: 2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25: 2 ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26: 2 CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27: 2 ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28: 2 ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29: 2 ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30: 2 ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31: 3 ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32: 3 ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33: 3 ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34: 3 ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35: 3 ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36: 3 ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37: 3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38: 3 ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39: 4 ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40: 4 ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41: 4 ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42: 4 ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43: 4 ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44: 4 ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45: 4 ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46: 4 ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47: 4 ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48: 4 ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49: 4 ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50: 4 ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51: 4 ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52: 4 ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53: 4 ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54: 4 ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55: 5 ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56: 5 ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57: 5 ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58: 5 ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59: 5 ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60: 5 NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61: 5 ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62: 6 ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 63: 6 ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 64: 6 ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 65: 7 ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 66: 7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 67: 8 ORF24 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 68: 8 ORF27 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 69: 8 ORF35 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 70: 8 ORF44 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 71: 8 ORF49 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 72: 8 ORF57 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 73: 8 ORF59 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 74: 9 ORF37 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 75: 9 ORF51 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 76: 10 ORF41 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 77: 10 ORF48 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 78: 11 ORF55 0.6118917 0.8437067 0.6974597 0.033505179 0.0189981734
## 79: 12 ORF64_1 0.5880849 0.8219482 0.7195606 0.034578844 0.0209653160
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002173813 -2.3786533 0.5530091 0.590266623
## 2: 0.002173813 -2.3786533 0.5530091 0.590266623
## 3: 0.002173813 -2.3786533 0.5530091 0.590266623
## 4: 0.002173813 -2.3786533 0.5530091 0.590266623
## 5: 0.002173813 -2.3786533 0.5530091 0.590266623
## 6: 0.002173813 -2.3786533 0.5530091 0.590266623
## 7: 0.002173813 -2.3786533 0.5530091 0.590266623
## 8: 0.002173813 -2.3786533 0.5530091 0.590266623
## 9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.004830169 -0.9381876 0.3682901 0.169040559
## 63: 0.004830169 -0.9381876 0.3682901 0.169040559
## 64: 0.004830169 -0.9381876 0.3682901 0.169040559
## 65: 0.005278328 -1.0831543 0.8420568 0.121609856
## 66: 0.005278328 -1.0831543 0.8420568 0.121609856
## 67: 0.005181368 -0.8929713 1.1657673 0.068980610
## 68: 0.005181368 -0.8929713 1.1657673 0.068980610
## 69: 0.005181368 -0.8929713 1.1657673 0.068980610
## 70: 0.005181368 -0.8929713 1.1657673 0.068980610
## 71: 0.005181368 -0.8929713 1.1657673 0.068980610
## 72: 0.005181368 -0.8929713 1.1657673 0.068980610
## 73: 0.005181368 -0.8929713 1.1657673 0.068980610
## 74: 0.005202505 -0.4915675 0.2569468 0.451195188
## 75: 0.005202505 -0.4915675 0.2569468 0.451195188
## 76: 0.005277337 -0.4694357 0.4086000 0.002664175
## 77: 0.005277337 -0.4694357 0.4086000 0.002664175
## 78: 0.004895109 -0.7634588 0.2463505 0.018100690
## 79: 0.004790086 -0.7521758 0.1706391 0.701623569
## se.bp v c pchi
## [1] "ORF61" "ORF74" "ORF46" "ORF62"## [1] 4## [1] "ORF4" "ORF5" "ORF9" "ORF38" "ORF50" "ORF63" "ORF65_1"
## [8] "ORF69" "ORF17" "ORF30" "ORF53" "ORF37" "ORF51" "ORF41"
## [15] "ORF48" "ORF55" "ORF64_1"## [1] 17Remove genes from clusters ?
## [1] "ORF4" "ORF5" "ORF9" "ORF38" "ORF50" "ORF63" "ORF65_1"
## [8] "ORF69" "ORF17" "ORF30" "ORF53" "ORF37" "ORF51" "ORF41"
## [15] "ORF48" "ORF55" "ORF64_1"## [1] 17## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 2 17
## 2: 4 16
## 3: 1 13
## 4: 3 8
## 5: 5 7
## 6: 8 7
## 7: 6 3
## 8: 7 2
## 9: 9 2
## 10: 10 2
## 11: 11 1
## 12: 12 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
